AMBER Archive (2004)

Subject: AMBER: IGR1/grnam1 problem

From: Marcin Krol (mykrol_at_cyf-kr.edu.pl)
Date: Tue May 18 2004 - 12:40:58 CDT

Dear All,
I'm trying to define a restraint on the distance between centres of
masses of two proteins.
My input file for MD is:
  run MD at 300K
 &cntrl
   ntc=2, ntf=2,
   cut=15.0, nrespa=2, igb=2, saltcon=0.2, gbsa=1,
   ntpr=100, ntwx=500, ntave=500,
   nstlim = 500000, dt=0.002,
   ntt=1, tempi=300.0, temp0=300.0, tautp=2.0,
   ntx=5, irest=1, ntb=0,
   nscm = 1000,
   nmropt=1,
   /
 &wt type='END' /
LISTOUT=REST.out
DISANG=RESTRAINT

and my original RESTRAINT file was:
#
# Definuje restraint na odleglosc pomiedzy sroedkami mas obu bialek
 &rst
 IAT = -1, -1,

 IALTD=1, r2=10, r3=35, r4=60, rk2=0, rk3=1,
 IRESID=1,
 IGR1= 2, 3, 4, 5, 0,
 GRNAM1(1)='CA', GRNAM1(2)='CA', GRNAM1(3)='N',GRNAM1(4)='N',
 IGR2=1, 1, 1, 1, 0,
 GRNAM2(1)='CA', GRNAM2(2)='CA', GRNAM2(3)='CA', GRNAM2(4)='CA',
 IR6=0,
 &end

This only works when IGR2 is always 1 and GRNAM2 is alwas 'CA'. When I try
to change it I get an error:
 Error: Too many atom ranges need to be stored for center-of-mass distance
        restraints. MAXGRP = 5. This needs to be increased.

I found a tutorial on the web
(http://structbio.vanderbilt.edu/comp/soft/amber/doc/html/AMBER-sh-6.14.html)
but it dosn't work in my case - I got the same error message as above.
However, I got it working when I changed IRESID to 0 and put numbers of CA
atoms in IGR1 nad IGR2. However, I am not sure what it actually does and
why I couldn't get it run with IRESID=1.
Thank you in advance for any comments
marcin

Dr Marcin Krol
Zaklad Bioinformatyki Collegium Medicum UJ
Kopernika 7E
31-501 Krakow
tel/fax (012) 422-77-64
e-mail mykrol_at_cyf-kr.edu.pl
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